Electrophoresis is used for a large number of applications. For example, DNA sequencing can be undertaken to determine the genetic composition, and specifically the nucleotide sequence, of a sample of DNA.
Many existing electrophoresis applications are undertaken using so-called "running tanks." In that procedure, a sample-containing gel is disposed in an electrophoresis chamber in the tank. Electric current is then applied to the gel by means of an electrode in the tank to cause electrophoresis of the sample. In the specific case of DNA sequencing, a thin slab of gel is disposed between two rigid glass plates, and this "gel sandwich" assembly is mounted vertically between upper and lower buffer chambers. A multiple-toothed "comb" structure is inserted into the gel to form "wells" adapted to receive samples. These "gel wells" are of uniform spacing and geometry (formats), as determined by the tooth geometry of the comb. Samples are conventionally deposited into the gel wells by means of nozzle dispensers. The most commonly used dispensers for electrophoresis applications are pipettes or syringes.
Vertical slab gel electrophoresis is the key separation technology used in the human genome effort currently underway. This project proposes to determine the sequencing of the entire human genome of three billion base pair within a five year period. Vertical slab gel electrophoresis, as currently practiced, incorporates an automated fluorescence DNA sequencer.
Sequencing technology has advanced rapidly. Standardization of equipment has been driven by the need for efficiency and reproducibility. A 96 well format has become the standard for manipulating and processing samples in the human genome project. The currently accepted sequencing protocol centers on this same standard 96 well format. This standardization has promoted efficiency in many areas of the human genome project, particularly in procedures involving the use of robotics. The 96 well format has been incorporated in a standardized 96 well sequencing tray, typically comprising a pipette tip rack. This rack has constituted the interface between the sample manipulation and electrophoresis loading steps of the overall procedure.
The loading of DNA samples onto the automated fluorescence DNA sequencer has not yet been automated, and thus remains a very labor intensive portion of the overall process. The loading step has constituted the most tedious part of the sequencing process. Individual samples have typically been deposited into the gel wells with a syringe equipped with a thin wire tip or with a pipette loaded with a flattened plastic tip. Recently, standardization to a 96 well format has facilitated the use of a multiple channel loader, based upon multiple syringes or a multi-channel pipette equipped with disposable tip strips. This multiple channel loading approach has greatly reduced the time and labor required for the loading step.
Samples are conventionally loaded into a sample rack in which individual sample wells are arranged in an array at target locations, each of which may be defined by unique Cartesian coordinates. These target locations are ordinarily disposed in ranks and files on a 96 format pattern; that is, 8 files of 12 ranks each. Advanced techniques involve loading an entire rank of 8 sample wells simultaneously with a multi-channel pipettor. The target locations of the respective sample wells has been standardized to 9 millimeters (mm), as has the spacing of the discharge tips of the multi-channel pipettors used to load those sample wells. The spacings of the comb teeth used to create the gel wells has also been standardized so that either 8 or 12 evenly spaced wells will register with the respective discharge tips of a standardized multi-channel pipettor.
Several standardized combs have evolved, each providing a fixed number of wells, or "lanes." A 36 lane comb produces lanes spaced such that a 9 mm eight-channel pipettor will register a tip with every other lane.; e.g., lanes 1, 3, 5, 7, 9, 11, 13 and 15. A second discharge pass of the pipettor registers with lanes 2, 4, 6, . . . and 16, thereby depositing sample into one half the available gel wells. The remaining half of the lanes (17-32) can then be filled in similar fashion. A 48 lane comb provides lanes spaced such that the nozzles of a 9 mm dispenser head register with every third lane (e.g., lanes 1, 4, 7, . . . and 22). Moving the dispenser head to fill wells at lanes 2 and 3 results in sample deposits into the first 24 wells, again one half the total number available. A 64 lane comb provides lanes spaced such that the 9 mm head registers with every fourth well. Depositing sample into wells 1 through 4 results in sample deposits to 32 wells, again one half the total available. In each case, the second half of the available lanes can be accessed by repeating the procedure applied to the first half of the available lanes.
It has been practical to utilize the sample racks and dispensers utilized for sample preparation in the electrophoresis operation as long as the formats of the sample arrays and gel well patterns have remained based upon the 96 sample well format, with 9 mm spacings. Unfortunately, as the press for greater through put has gained momentum, the spacings between gel wells has been further decreased, and standardization based upon the 96 well format has been abandoned with respect to the electrophoresis operation. Recently, a 96 lane comb has been introduced. While a 9 mm head will register with every fifth lane (1, 6, 11 . . . 36) produced by this comb, deposits to wells 1 through five accounts for a total of 40 lanes. Repeating the procedure accounts for only 80 of the 96 available lanes, leaving 16 lanes which must be accessed by some other means. Reliance upon the conventional 9 mm head is thus inappropriate. Accordingly, there has evolved a new standard multi channel dispenser format for the loading of gel wells produced by the new 96 lane combs. This dispenser has eight nozzles spaced 10.8 mm so that individual dispenser tips access every seventh lane. Deposits into wells 1 through 6 effects deposits into a total of 48 wells, one half the 96 available lanes.
Because the existing standard 96 sample well format does not interface with the 10.8 mm pipette head spacing imposed by the new 96 lane comb used for gel well formation, adoption of this new electrophoresis format imposes a requirement for reformatting the sample array prior to the electrophoresis loading step. This step is relatively labor intensive and time consuming. It also introduces an additional opportunity for error in the overall procedure. It is economically unfeasible to retrofit all of the extant laboratory facilities currently wedded to the 96 well sample format to adopt a 10.8 sample well spacing.